Curator Dashboard

Offers access to instrumentation, training, and service using advanced light microscopy, scanning electron microscopy, and transmission electron microscopy. Provides access to core imaging and analytical characterization technologies. In addition to instrument access, SRNML personnel offer advice, hands-on training, education, and research collaboration. Provides range of sample preparation equipment.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Core facility that provides the following services: Flow cytometry analysis service, Cell cycle analysis, Cell sorting service, Side population cell sorting, Zebrafish cell sorting and analysis. The Stem Cell Core Facility has been part of the IDDRC center for more than 30 years fostering collaboration and innovation among IDDRC investigators and members of the academic research community. It was used to develop chromosome sorting for human chromosome specific recombinant libraries and these techniques were utilized by others to generate large scale libraries for the early genome project. The facility was the first to develop cell sorting of fetal cells in the maternal circulation as a means to detect fetal genetic abnormalities. Throughout its history the Stem Cell Core has provided careful and accurate cell cycle analysis via DNA content analysis using Hoechst dye uptake. This service is still used today by investigators. The facility was among the first to take advantage of the ability to express GFP in cells transfected with vectors and induced to express GFP in transgenic animals conditionally expressing a specific gene promoter. This ability allowed IDDRC investigators to isolate neurons, muscle cells and other cell types which express GFP from those which do not. IDDRC investigators were among the first to subsequently culture sorted neurons. Based on the extensive experience of the core using Hoechst dye for cell cycle analysis, the core was able to help IDDRC investigators prepare side population cells (tissue derived potential multipotent progenitor cells) based on Hoechst dye efflux. These methods have allowed the isolation of different muscle side population cells and have facilitated experiments that aim to use the cells for treating muscle disease. The interactive and collaborative nature of the core has fostered these developments, and the interests of the core director, advisory committee, manager and IDDRC investigators will continue to make this core as innovative in the future as it has been in the past. The overall goal of the Stem Cell Core Facility is to provide both IDDRC and non-IDDRC researchers comprehensive analytical flow cytometry and cell sorting services in a timely, dependable and cost-effective manner., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 13 years ago - by Anonymous

Services include use of high throughput screening technology, compounds in various libraries, siRNA sets of druggable genome for mouse and human and database of results from screens. For compounds screens, data points are in singlets.For functional genomics screens we use duplicates. We typically utilize 384 well plates but are flexible in this regard. We can accomodate any plate type ranging from 96 to 1536 well plates. Specialty plates can be handled on needed base. We have special rates for consumables with many vendors based on volume we use. These reduced rates are passed on directly to our screeners.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Core facility that provides the following services: Data collection, data entry and analysis, Database design, data management and process tracking, Qualitative data collection, management and analysis.

The Survey and Data Management Core (SDMC) provides efficient, high-quality survey data collection and management services and consultation to support the research needs of investigators and staff throughout the Harvard Medical research community. The Core, housed within the Center for Population Sciences at the Dana-Farber Cancer Institute, is dedicated to rigorous quantitative and qualitative survey data collection and management.

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• SciCrunch
• 13 years ago - by Anonymous

Sotware R package for differential discovery analyses in high dimensional cytometry data including flow cytometry, mass cytometry or CyTOF, and oligonucleotide tagged cytometry.

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• RRID
• 4 years ago - by Anonymous

Core facility that provides the following services: Cell sorting service, Cell analyzing service, Cell separation service, Cell cytometer service, Data services, Flow cytometry protocol development service, Benchtop flow cytometry analyzer training, Flow cytometry beta-testing service. Committed to meet all of the flow cytometry needs for the BIDMC and the external research community, the Flow Cytometry Core facility offers state of the art instrumentation for routine flow cytometry and cell sorting. It is continuously expanding with the newest software and machinery for both sort and analysis capabilities of up to 30 flourescent parameters. The Flow Cytometry Core facility is available to: answer technical questions; assist you in setting up flow cytometry experiments; assist you with acquiring, analyzing and interpreting your data; assist in data presentation and data storage; provide training on the four benchtop analyzers and on software. To schedule an appointment for regular flow cytometry (user operated), log onto our online web calendar at: http://bidflow.calendarhost.com/

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• SciCrunch
• 13 years ago - by Anonymous

Open source, community curated registry, meta-registry, and compact identifier resolver. Used for unifying identification of biomedical entities through integrative, open,community driven metaregistry. The registry contains metadata about ontologies, controlled vocabularies, and resources including their preferred prefix, name, description, homepage, mappings to other registries, and more.

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• RRID
• 4 years ago - submitted by Charles Hoyt

The Clinical Genetic Research Facility (CGRF) offers clinical investigators a convenient, modern research-dedicated facility for outpatient studies involving genetics. Our outpatient exam rooms and phlebotomy rooms are fully equipped and offer investigators an experienced medical assistant to facilitate the visit. Since the CGRF?s primary mission is to support and promote genetic clinical research, the facility?s investigators performing genetic studies supported by non-commercial sponsors are given priority. The CGRF also considers genetic studies sponsored by industry, as well as studies without a genetic component, on a space-available basis.

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• SciCrunch
• 13 years ago - by Anonymous

Research education program to build sustainable national workforce of rehabilitation researchers equipped with basic data science skills in five years.

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• NIF
• 4 years ago - by Anonymous

An efficient software tool to connect overlapping pair-end reads using k-mer frequencies.

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• SciCrunch
• 12 years ago - by Anonymous

Software tool that scores positions in human genome in terms of their regulatory probability. Regulatory Mendelian Mutation score was created for relevance prediction of non-coding variations (SNVs and small InDels) in human genome (hg19) in terms of Mendelian diseases.

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• RRID
• 4 years ago - submitted by Max Schubach

A platform composed of three modules: the Database, the Search Engine, and rSNPs, for the computational identification of transcription factor binding sites (TFBSs) in multiple genomes, that combines TRANSFAC and JASPAR data with the search power of profile hidden Markov models (HMMs). The Database contains putative TFBSs found in the upstream sequences of genes from the human, mouse and D.melanogaster genomes. For each gene, they scanned the region from 10,000 base pairs upstream of the transcript start to 50 base pairs downstream of the coding sequence start against all their models. Therefore, the database contains putative binding sites in the gene promoter and in the initial introns and non-coding exons. Information displayed for each putative binding site includes the transcription factor name, its position (absolute on the chromosome, or relative to the gene), the score of the prediction, and the region of the gene the site belongs to. If the selected gene has homologs in any of the other two organisms, the program optionally displays the putative TFBSs in the homologs. The Search Engine allows the identification, visualization and selection of putative TFBSs occurring in the promoter or other regions of a gene from the human, mouse, D.melanogaster, C.elegans or S.cerevisiae genomes. In addition, it allows the user to upload a sequence to query and to build a model by supplying a multiple sequence alignment of binding sites for a transcription factor of interest. rSNPs MAPPER is designed to identify Single Nucleotide Polymorphisms (SNPs) that may have an effect on the presence of one or more TFBSs.

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• SciCrunch
• 17 years ago - by Anonymous

Core offers specialized expertise for analysis of proteins and peptides using mass spectrometry. Develops new methods and customized approaches for proteomic analysis and suggests experimental strategies and sample preparation prior to mass spectrometry analysis. Services include:comprehensive protein identification ,analysis of affinity purified complexes,characterizing protein post-translational modifications,de novo sequencing,label and label-free quantitation ,multiplexed quantitation global phosphorylation and ubiquitin analysis,analysis of laser-capture microdissected formalin-fixed paraffin-embedded tissue,secretome analysis,crosslinking analysis,disulfide mapping.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

The Oomycete Genomics Database is a publicly accessible resource that includes functional assays and expression data, combined with transcript and genomic analysis and annotation. OGD builds upon data available from the Phytophthora Genome Consortium, Syngenta Phytophthora Consortium and the Phytophthora Functional Genomics Database. Data are analyzed and annotated using NCGR''s XGI System. The knowledge gained from these studies provide significant insight into key molecular processes regulating an economically important pathosystem and will provide novel tools for improvement of disease resistance in crop plants.

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• SciCrunch
• 17 years ago - by Anonymous

AMRDC Repository provides archival, preservation, access, and metadata authoring services for Antarctic meteorological data, managing data from submission to end-user retrieval. The repository hosts data collected by the Antarctic Meteorological Research Center and Automatic Weather Station projects, as well as campaign meteorological datasets deposited by other Antarctic investigators.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Software tool to evaluate de novo genome assemblies with RNA transcripts.

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• SciCrunch
• 13 years ago - by Anonymous

Provides open access to Climate and Earth System Data from scientists at the centre and their collaborators. Helps to make your data open, FAIR and visually appealing. Each dataset and source code in the Bolin Centre Database is assigned a unique DOI. This makes it easy to cite and find your data. If dataset has more than one version, each version will have its own DOI.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 08, 2013. A repository for physical mapping data of the human X chromosome that aims at providing a global view of genomic data at a chromosomal level including an integrated physical, genetic, transcript and sequence map of the human X chromosome. This implies acquiring, understanding and formatting an enormous amount of experimental results and can only be accomplished progressively. We have chosen to start the integration process with YAC maps generated by the community. These provide the basis for future higher resolution physical maps, as well as emerging transcript and sequence maps. The current content of IXDB therefore reflects this situation, with the emphasis placed on YAC mapping data. Due to their immediate value, IXDB has also started to systematically include bacterial clone contig maps and EST data. Currently IXDB does not store sequence data, although links to nucleic sequence databases are provided.

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• SciCrunch
• 15 years ago - by Anonymous

Core facility is available for use by any researcher at university whose work requires manipulation of biological agents that may cause serious or potentially lethal disease as result of exposure by inhalation route.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Portal and tools for sharing and editing neurophysiological and behavioral data for brain-machine interface research. Users can search for existing data or login with their Google, Facebook, or Twitter account and upload new data. Their main focus is on supporting brain-machine interface research, so we encourage users to not just provide recordings of brain activity data, but also information about stimuli, etc., so that statistical relationships can be found between stimuli and/or subject behavior and brain activity. The Matlab tools are for writing, reading, and converting Neuroshare files, the common file format. A free, open source desktop tool for editing neurophysiological data for brain-machine interface research is also available: https://github.com/ATR-DNI/BrainLiner Since data formats aren''''t standardized between programs and researchers, data and analysis programs for data cannot be easily shared. Neuroshare was selected as the common file format. Neuroshare can contain several types of neurophysiological data because of its high flexibility, including analog time-series data and neuronal spike timing. Some applications have plug-ins or libraries available that can read Neuroshare format files, thus making Neuroshare somewhat readily usable. Neuroshare can contain several types of neurophysiological data, but there were no easy tools to convert data into the Neuroshare format, so they made and are providing a Neuroshare Converter Library and Simple Converter using the library. In future work they will make and provide many more useful tools for data sharing. Shared experiments include: EMG signal, Takemiya Exp, Reconstruct (Visual image reconstruction from human brain activity using a combination of multi-scale local image decoders), SPIKE data, Speech Imagery Dataset (Single-trial classification of vowel speech imagery using common spatial patterns), Functional Multineuron Calcium Imaging (fMCI), Rock-paper-scissors (The data was obtained from subject while he make finger-form of rock/paper/scissors). They also have a page at https://www.facebook.com/brainliner where you can contact us

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• SciCrunch
• 16 years ago - by Anonymous